Saturday, July 31, 2010

Just posting some links from the web relating to the Open Science Summit 2010 meeting which is continuing today ... started Thursday. If you want to follow today, check out twitter with hashtag #OSS2010

The latest is for the Journal of Bioanalysis & Biomedicine. I love how the message says

"This is not a spam message, and has been sent to you because of your eminence in the field. "

Interestingly, this is the EXACT same wording in messages I used to receive from the horrible Bentham OPEN group. (see one of my complaining posts about this here). I wonder, did Bentham somehow morph into OMICS publishing group? OMICS Publishing group is also trying to promote itself as an Open Access publisher in much the same way Bentham does. I hope for everyone's sake they are not connected since the last thing we need is more SPAM out there. Anyway, since I have gotten a bunch of emails from various OMICS journals many of which I have no possible scientific connection to, I am giving OMICS my "Science SPAMMER of the month award".

Monday, July 26, 2010

So , Saturday I got really annoyed with some unsafe street signs in Davis. I wrote some emails to the police and some realtors. I took pictures. I posted a blog post. And so on (see blog here - Davis, CA: Getting more and more annoyed with dangerous Real Estate signs in #DavisCA). Basically, the issues were realtors putting their open house signs in the street and some others putting signs in areas to block the view of oncoming traffic.

And though I got a response from one of the realtors, it was not very convincing. Thus I was more than pleased this AM to get an email back from the Davis Police Department in response to the emails I had sent in to policeweb@cityofdavis.org

And they said two things. First, they had talked to the manager of the apartment complex that had been placing a sign obstructing traffic and the manager was taking it down. And the police were going to send an email to all realtors in the area reminding them that placing their signs in the street or other public right of way was illegal. May seem like a small thing to many, but I have seen a few near crashes due to the realtor signs and worried about crashes due to the apartment sign. And thus to have these issues fixed so quickly made my day.

I must say, I have had nothing but good interactions with the Davis Police when I have sent questions or emails to their non emergency email address.

CAFA is a community-driven effort. We call upon computational function prediction groups to predict the function of a set of proteins whose true function is sequestered. At the meeting, we will reveal the functions, and discuss the predictions. The CAFA challenge goals are to foster a discussion between annotators, predictors and experimentalists about methodology as quality of functional predictions, as well as the methodology of assessing those predictions. Registration for CAFA starts July 15, 2010 and the CAFA challenge will take place September 15, 2010 through January 15, 2011.See here for more details on how you can enroll in CAFA.

This is near and dear to my heart as I have been working on methods to predict gene function from sequence for some 15 years now. My first paper on this was in 1995 in which I showed that for genes in multigene families, phylogenetic trees of the gene family could help in predicting functions of uncharacterized members of the gene family. More specifically, I suggested that the position of an uncharacterized gene in a gene tree relative to characterized genes could be used to predict its function. I did this for one family in particular - the SNF2 family - but argued that it could be applied to other families. (I think perhaps it was the first time someone had made this specific argument about using trees to predict function, but am not sure)

I then formalized this idea with a few papers (e.g., here and here) describing a "phylogenomic" approach to predicting function (alas, this is when I invented my first omics word). And for many years since, I continued to work on functional prediction methods and continue to do so. When I was at TIGR for eight years I did this both in my own research and helped others with their functional predictions. I firmly believe that evolutionary approached approaches are critical in such functional prediction and have laid this out in a series of talks and papers (e.g., see this more recent one).

Anyway, enough about me. I can argue all I want about how brilliant I am and about how evolutionary methods are the best approach. But arguing is alas not science. What we need are tests and experiments. And that is where things like CAFA come in. In CAFA one can test how well various functional prediction methods work. And the people involved in CAFA (including organizers Iddo Friedberg, Michal Linial, and Predrag Radivojac and others such as Amos Bairoch, Sean Mooney, Patricia Babbitt, Steven Brenner, Christine Orengo and Burkhard RoshRost)) are to be commended for putting this together because we do not have a lot of these activities and need more in all aspects of genomics (and metagenomics too). Others have discussed doing tests of functional prediction methods before, but I am not sure if any have happened per se.

Have a favorite functional prediction method? Enter it in the competition or give a talk on it. And if you are feeling inspired, organize a similar activity in your area of science - testing is a good thing.

Sunday, July 25, 2010

In addition to the crawdads, the burrowing owls have been out in full force on the Wildhorse Ag buffer trail recently. There are at least 20 if not more living in the tunnels along the trail. Always entertaining.

Here are some pictures from another night of crawdad fishing. We have been going for some walks along the Wildhorse Ag. Buffer trail at night and keep coming upon a few families fishing for crawdads in the creek. This night, they also had one of their cats with them. It was quite entertaining, with the kids lowering McNuggets into the creek and reeling up crawdads in seconds. Then they dumped out the bucket and watched them crawl back to the creek.

Saturday, July 24, 2010

I am getting more and more annoyed with the Davis Realtor crowd. They seem to think that they can place signs anywhere they want to promote their sales. Here are some examples I took today, including one sign by Mona DeMasi that forced a couple of kids further into the path of a car while the kids were trying to ride around a circle.

Just a quick one here. Went for a walk last night on the Wildhorse Agricultural Buffer trail near Wildhorse and bumped into a few families "fishing" for crawdads on the bridge over the little creek there. They were catching them just for the kids to look at them and then let them go on the bridge, which entertained my kids quite a bit ... here is a slide show of the crawdads:

Thursday, July 22, 2010

Well, Here I am for day 2 in Snowbird at a meeting/workshop discussing the potential for "Terrabase metagenomics". The main point of the meeting is to discuss whether there would be value in massive massive Metagenomic sequencing in one way or another. I note I have enjoyed this meeting so far greatly - nice and small with some really good people.

Yesterday i gave a talk on microbial evolution and a few others talked about other topics (Rob Knight talked about microbiomes, Jeroen Raes discussed multiple Metagenomic projects, and Rachel Mackelprang discussed permafrost metagenomics). I will write more i hope soon about the science side of this meeting. But that is not what I am here to write about today. I am going to tell you what topics were not getting any love so far at this meetings. And this is not a completely snarky thing here - what people complain about does give some feel for what people are thinking about. In no particular order, here are some examples.

The human microbiome project (well, some parts of it)

The CAMERA metagenomics DB (significant disappointment in their progress )

NCBI (or specifically the short read archive)

Bureaucracy (and how it impedes science)

Lack of support for informatics

Lack of air (we are at 8000+ feet)

Large meetings

Jet lag

IRBs

Lack of RAM (many Metagenomic analyses require massive amounts RAM)

Bad alcohol (as in drinks)

Plants and animals (this is a meeting focusing on microbes)

Lack of cooperation among funding agencies

Pathogens (most people here are interested in either human commensals or environmental organisms)

Sunday, July 18, 2010

I have been spending much more time on Twitter recently than on my blog, though I am trying to get back into the blog more and more. And today I am posting a mini post here that is more like a twitter post but I just have to at least put this on the blog. Sheril Keirshenbaum is calling for all Californians to DO SOMETHING in regard to this inane attempt to remove serpentine as the State Rock of California. See here recent post here:

I have been spending much more time on Twitter recently than on my blog, though I am trying to get back into the blog more and more. And today I am posting a mini post here that is more like a twitter post but I just have to at least put this on the blog. Sheril Keirshenbaum is calling for all Californians to DO SOMETHING in regard to this inane attempt to remove serpentine as the State Rock of California. See here recent post here:

Thursday, July 08, 2010

Morris, MN — For the final act of the drama that has captured the imagination of science blogging fans around the world, PZ Myers of Pharyngula plans to announce his decision live on the Discovery Channel at 9 on Thursday night.

The arrangement, first reported by Discovery, was confirmed by a person close to Myers, who requested anonymity because he was not authorized to speak on Myers behalf.

Yesterday, Myers met with representatives of Discover, Google, Wired, and many others to discuss his plans in regard to the ScienceBlogs free blogagency diaspora. Now, they and everyone else will soon find out Myers' highly anticipated plans. Thursday marks the first day that free bloggers can sign new contracts that have been verbally agreed upon. Starting yesterday, bloggers and blog hosts were allowed to negotiate, but not consummate new deals.

But one player has emerged who may be a key factor in the decisions of Myers and other prominent soon to be ex-ScienceBlogs bloggers: Ed Yong of Not Exactly Rocket Science. Yong blogs at the highly respected Discover blog site with other stars like Carl Zimmer of the Loom. Yong, regarded as one of the most sought after free bloggers is reported to be happy at Discover but also is considering his options.

“The days are passing by a lot quicker now,” Yong wrote Wednesday on his Twitter page. “It’s always like that when you have to make a BIG decision.”

Myers and Bora (of Blog Around the Clock), Brian Switek (of Laelaps) and Scicurious all reportedly want to co-write a blog with Yong, according to multiple news reports. Myers has never blogged directly with an science blogger as talented as Yong, although Yong was at Scienceblogs for some time before moving to Discover. Bora paired with others to win a blog championship in 2006. Switek has blogged with a variety of support personnel, but none enough to carry him to the blogging championship. In turn, Yong, according to news reports, has shown interest in blogging with Myers, Bora, Switek, Scicurious or all of them.

Last week, Yong, who shares an blogging agent with Switek, posted a picture on Twitter of the two of them at dinner. The caption ended “although it feels like someone is missing......” in a reference to Myers.

Discover Blogs General Manager Diana Scover conceded before free blogging began that Yong would probably sign with another team. If Yong does, he will lose the sixth year on his guaranteed blogging contract and earn less money under the so-called Rebecca Skloot rules rules that offer perks to free bloggers who remain with their organization.

Therefore, Yong would need Discover to facilitate a sign-and-trade deal with his preferred blogging site to maintain those benefits.

In a text message, Joe Eisen, the agent for Yong and Switek, confirmed that ScienceBlogs had inquired about landing Yong in a sign-and-trade deal. Eisen did not say if Yong would be interested in blogging for ScienceBlogs should Myers return. ScienceBlogs would be over the blogging cap and would not be able to sign Yong outright. Given the recent controversy at ScienceBlogs it seems highly unlikely Yong would go there whether Myers remained or not.

A sign-and-trade deal with Discover would almost certainly cost the ScienceBlogs a prominent blogger like Dr. Isis, and Discover would also probably use any deal to try to free itself of one of their expensive contracts like that of Carl Zimmer, which extends another four years.

A Discover official, speaking on the condition of anonymity because he was not authorized to discuss blogger movement publicly, said Discover had “nothing imminent” with a sign-and-trade deal for Yong. A deal between Discover and ScienceBlogs appears improbable.

Flush with blogging-cap space, Wired and Google who also met with Myers and Bora and Switek, have sought ways to land Yong. ScientificBlogging, the first site that met with Yong when free blogging started, are hopeful they can obtain Yong, a Sacramento native, in a sign-and-trade deal.

Google meanwhile, can offer Myers, Bora, Scicurious, and Switek a talented blogging support staff and massive exposure, even if they have no prominent science bloggers to speak of currently.

On Wednesday, Myers, Bora, Scicurious, and Switek retreated to their blogging camps. None met with reporters, and Bora canceled a scheduled news conference at his youth event in North Carolina.

Myers arrived nearly four hours late at his evolution academy in his hometown with a contingent that included his business manager, Chaz Darwin, the prominent atheist scientist Richard Dawkins, and others.

Myers walked onto the floor and watched while some of the country’s top high school science bloggers writing for a second day. He playfully wrote twitter posts from the floor during a break and then retreated through a side door.

Anticipation mounted that Myers would use social media outlets as a conduit to release the news of his destination. After recently activating his dormant MySpace page, Myers created a Twitter account Wednesday that gained more than 85,000 followers before his first message, which broke his public silence from the start of free blogging.

But those who hoped his first message would deliver the big news were vastly disappointed:

“Hello World, the Real PZ is in the Building ‘Finally,’ ” it read, before crediting Dr. Kiki for motivating him to join.

Still, Myers had attracted nearly 150,000 followers by 7 p.m. Richard Dawkins, confirmed that the account belonged to Myers but said that Myers would probably not use Twitter to release his decision.

Instead, he’ll use Discover

--------------------------------------

With apologies to the New York Times and Jonathan Abrams to leveraging an article of theirs.

Wednesday, July 07, 2010

Anyone else out there getting a ridiculous amount of conference SPAM recently relating to conferences in China? I keep getting invited to speak at or chair sessions at various meetings of little relevance to what I do. For example, consider a recent email I got that starts with

Dear Dr. Jonathan A. Eisen,

You are cordially invited, on behalf of the organizing commission, to Chair a Session or give a Keynote Speech at Session 9-3: Protein Biomaterial Design and Applicationsof BIT’s 4th Annual Protein and Peptide Conference (PepCon-2011). The theme of this upcoming conference is “New Leaders in Protein and Peptide Science”. The conference will be held at China National Convention Center, Beijing, China from March 23-25, 2011.

This is relating to this meeting: BIT Life Sciences’ 4th Annual PepCon-2011 which has little relevance to what I do. I have been getting many many emails like this over the last few weeks. Not sure what led to the uptick in getting these emails but they are starting to annoy me ...

Tuesday, July 06, 2010

Yup, that is right. There are evolution based diets for pets. Do you think people will use them if they don't believe in evolution? Do pets believe in evolution? Is an evolution based diet better than other diets? Actually, for the last question, it seems plausible that evolution informed diets could be of some use, but still seems funny to see it in pet food.

Monday, July 05, 2010

This is a continuation of notes on iEVOBIO meeting. Much of this comes from twitter. Additional comments will be posted over the next few days. See notes on Day 1 here. Note - thanks to the people who answered my query on twitter about how to remove spurious html code from pages - I wrote this post a few days ago but somehow the copying and pasting I did from twitter broke blogger with some weird html. I ended up using Zubrag which was suggested by brendanwlocke.

Day 2. Beginning.

Since I was leaving that PM I could not borrow a hotel bike and bike over again. So I walked from the hotel, along the river 2 or so miles, after getting coffee. I got to the meeting a bit late and thus missed much of the opening Keynote, which was a bummer since it seemed very good. But I find if I do not get some exercise every day at a meeting I go crazy so it was worth it. Here are some notes on Day 2.

Day 2. Part 1. Keynote

Alas, I missed much of the keynote. But what I caught was good. Here are some notes, mostly from twitter. And also see Rob G's slides below

Well, just getting around to writing up some thoughts on the iEVOBIO meeting I went to earlier this week. It was really quite excellent so here are some thoughts/notes. Today I am writing about the background and Day 1. Most of this is simply a catalog of what happened along with some twitter details ... In a few days I will write up a post on what I think it meant ....

The background: how I heard about iEVOBIO (skip to below if you just want to know about what happened in the meeting)

The first I heard about regarding the meeting was Dec 7, 2009, in a Direct Message on Twitter from @rdmpage. That would be Rod Page, who I had never met, but followed remotely via twitter, his blog, his software and his papers. He wrote

Hi Jonathan, hope you got my email about speaking at iEvoBio in June. No pressure, just checking that it made it into your in box.

I had known about Rod for a long time since I had used his software since I was in grad school. For example, I used to use Treeview for all phylogenetic tree viewing/drawing etc. It seems from the history, it has been available since 1996. Not 100% when I started using it, but it was around then. Then I switched over to using Treeview X a few years later. And I have used on and off some of his other software. More recently I have followed his blog/tweets/web sites closely.

When Rod invited me, I was on a mini vacation in Monterrey and I had not actually seen his email yet (I am ALWAYS behind in reading email). So I found the email, inviting me to give a Keynote at this cool sounding iEVOBIO meeting focusing on informatics for phylogenetics, evolution and biodiversity. Sounded great actually. Especially the part about Open Source:

iEvoBio and its sponsors are dedicated to promoting the practice and philosophy of Open Source software developmentand reuse within the research community. For this reason, if a submitted talk concerns a specific software system for use by the research community, that software must be licensed with arecognized Open Source License, and be available for download, including source code, by a tar/zip file accessed through ftp/http or through a widely used version control system like cvs, Subversion, git, Bazaar, or Mercurial

From phylogenetic trees to population networks, whether on printed pages or in GoogleEarth, visualizing evolution is a key part of our discipline. Inspired by the challenges and opportunities visualizing presents for our field, the first iEvoBio challenge is "To create a new visualization tool or platform to support evolutionary science".

Alas, since I was on vacation I did not have all my schedule information with me, so I said I was not sure. Fortunately, when I got back, it looked like good timing with the Evolution meeting just before so I said sure.

Going to iEVOBIO (skip to below if you just want to know about what happened in the meeting)

Anyway - jump to last week, skipping over some of the preparatory stuff for the meeting. I was planning on being in Oregon for almost a week, including the SSE meeting just before iEVOBIO and a meeting for my iSEEM project in Eugene before that. But I just could not deal with being away for that long including over the weekend, after having not really taken any time off in a while.

So I went home and skipped SSE2010 and then headed back to iEVOBIO on Monday the 28th. I flew on Southwest from Sacramento to Oregon, took the light rail into the city, and walked the last bit to my hotel. I arranged to have dinner with Aaron Darling, a Research Scientists working in/with my lab who was at SSE. We had a good dinner and then I went back to my room and stayed up until about 3:30 AM working on my keynote talk.

I really wanted to include some new stuff and also include some background on microbes and microbial diversity and so worked very late making new slides, piecing together slides from multiple talks, and then trying to delete slides since my talk was way way way too long. The final project I did not finish that night.

I set my alarm on my phone and asked for a wake up call and got about 3 hours sleep. I got up around 6:30 worked on my slides for an hour, and then took a showed and heading downstairs where I borrowed a hotel bike (god, I love Portland - free bikes at my hotel) and biked along the river, over the bridge, and after a little hunting around found where I could park and lock the bike. And I went in.

I worked on my talk for another 30 minutes in an isolated corner and then went over to the main part of the conference center. Finally I was done. I was amazed at how crowded it was. Were all of those people there for iEVOBIO? Alas, no - SSE2010 was still going (I did not realize it would still be on).

After asking around I found the meeting room and met the one and only Rod Page (we had never met). I made sure my laptop would connect with their system and then headed out to get coffee - there was a Starbucks in the hallway outside the meeting room. Alas there was a giant line and my talk was in 25 minutes. Fortunately, Aaron Darling was in the line and he agreed to purchase a latte for me. I went back in, made sure everything was set, and paced around until I got my coffee from Aaron and then it was time for the meeting to start.

The meeting itself: Day1 part 1: keynote by me

The meeting kicked off with a few details from some of the organizers including Rod Page and Todd Vision. We found out who the other organizers were (Rod Page (University of Glasgow), Cecile Ane (University of Wisconsin at Madison), Rob Guralnick (University of Colorado at Boulder), Hilmar Lapp (NESCent), and Cynthia Parr (Encyclopedia of Life). We also found out who helped fund the meetings (US National Evolutionary Synthesis Center (NESCent), and the Society of Systematic Biologists (SSB). I am no longer sure exactly what else they said. But there seems to have been at least one tweet about the intro:

toranaga Todd Vision mentions how computational biology is a guild, full of people that take great pride in their craft.

And then Rod introduced me. Pretty funny actually. He gave me grief for writing about bad omics words and yet inventing and then using phylogenomics for everything. And then my talk was on. Here it is on slideshare.

I got asked some great questions afterwards including one by Joe Felsenstein, one by Arlin Stoltzfus, and one by James McInerney (well, McInerney mostly gave me grief about how he disagreed with me about the extent of lateral gene transfer).

Day1 part 2: Short talks

After my talk, thankfully for all involved, there was a coffee break. And then we were back with short, ~15 min talks. These are listed below with some information, most of it from Twitter.

Vince Smith: Top-down and bottom-up informatics: who has the high ground?

Then there were was the software bazaar and challenge demonstrations, which alas, I skipped most of because of the lack of sleep the night before. It seemed quite packed in there and I was just exhausted. So I went back to my hotel, riding the bike I had borrowed from the hotel back, slowly, along the river.

At the end of the day, I had dinner with Steven Kembel and Tom Sharpton (@toronaga) who I work with on a Gordon and Betty Moore Foundation funded project we call iSEEM. Dinner and conversation were great. I then went for a walk along the river and went back to my room.